/ 
Bio-EnsEMBL-112.0_52
River stage zero No dependents
/ Bio::EnsEMBL::Analysis::PairAlign

LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

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NAME

PairAlign - Dna pairwise alignment module

SYNOPSIS

#To convert between coordinates:

my $cdna_coord = $pair->genomic2cDNA($gen_coord);
my $gen_coord  = $pair->cDNA2genomic($cdna_coord);

DESCRIPTION

Contains list of sub alignments making up a dna-dna alignment

Creation:

my $pair = new Bio::EnsEMBL::FeaturePair(
  -start  => $qstart,
  -end    => $qend,
  -strand => $qstrand,
  -hstart => $hstart,
  -hend   => $hend,
  -hend   => $hstrand,
);

my $pairaln = new Bio::EnsEMBL::Analysis::PairAlign;
$pairaln->addFeaturePair($pair);

Any number of pair alignments can be added to the PairAlign object

eachFeaturePair

Title   : eachFeaturePair 
Example : my @pairs = $pair->eachFeaturePair
Returns : Array of Bio::SeqFeature::FeaturePair
Args    : none

genomic2cDNA

Title   : genomic2cDNA
Usage   : my $cdna_coord = $pair->genomic2cDNA($gen_coord)
Function: Converts a genomic coordinate to a cdna coordinate
Returns : int
Args    : int

cDNA2genomic

Title   : cDNA2genomic
Usage   : my $gen_coord = $pair->genomic2cDNA($cdna_coord)
Function: Converts a cdna coordinate to a genomic coordinate
Example : 
Returns : int
Args    : int

convert_cDNA_feature

Title   : convert_cDNA_feature
Usage   : my @newfeatures = $self->convert_cDNA_feature($f);
Function: Converts a feature on the cDNA into an array of 
          features on the genomic (for features that span across introns);
Returns : Array of Bio::EnsEMBL::FeaturePair
Args    : Bio::EnsEMBL::FeaturePair